CIViC MCP Server

What is CIViC MCP Server?

This Cloudflare Workers-based MCP server provides tools for querying the CIViC (Clinical Interpretation of Variants in Cancer) API. It converts GraphQL responses into queryable SQLite tables using Durable Objects, enabling AI assistants to analyze cancer genomics information through natural language.

How to use CIViC MCP Server?

Deploy the server to Cloudflare Workers (npm install && npm run deploy), then configure Claude Desktop with mcp-remote pointing to the deployed URL. Once configured, Claude can use three tools: civic_graphql_query, civic_query_sql, and civic_execute. Three MCP prompts (get-variant-evidence, get-variant-assertions, get-variant-data) guide the model with correct GraphQL syntax.

Key features of CIViC MCP Server

• GraphQL to SQL conversion into structured SQLite tables
• Efficient data storage via Cloudflare Durable Objects with SQLite
• Smart response handling: bypasses staging for small, error, empty, or schema introspection responses
• Tool pipeline: GraphQL query, SQL analysis, and Code Mode (JavaScript execution)
• MCP 2025-06-18 compliance with Streamable HTTP transport
• Three MCP prompts for guided, fallback-aware GraphQL queries

Use cases of CIViC MCP Server

• Query the latest evidence items for specific mutations (e.g., BRAF V600E)
• Retrieve therapeutic interpretations for lung cancer variants
• Find genes with the most evidence items in the CIViC database
• Analyze staged data using custom SQL queries
• Use Code Mode to run JavaScript against the CIViC GraphQL API in a V8 isolate

FAQ from CIViC MCP Server

What is the CIViC database?

CIViC (Clinical Interpretation of Variants in Cancer) is a crowd-sourced repository of clinical interpretations of cancer variants.

What tools does the server provide?

Three tools: civic_graphql_query (execute GraphQL queries), civic_query_sql (query staged data with SQL), and civic_execute (run JavaScript in a V8 isolate with full GraphQL access).

How do I deploy the server?

Requires a Cloudflare account and Wrangler CLI. Clone the repository, run npm install, then npm run deploy. After deployment, use the obtained URL in Claude Desktop configuration.

What transport protocol does the server use?

It uses Streamable HTTP transport (MCP 2025-03-26+) served at the /mcp endpoint. Legacy HTTP+SSE transport has been removed.

Is OAuth 2.1 authorization supported?

OAuth 2.1 is not implemented yet. The README notes it as pending action, requiring Authorization Server discovery, Resource Indicators (RFC 8707), and PKCE-enabled authorization code flow.